Year Total Jaccard Dissimilarity Models

This code is Script 4d for Kitchel et al. “Biotic homogenization, the exception and not the rule for marine fish communities” manuscript.

• This project is a collaborative effort to describe changes in taxonomic composition of fish communities around the world–as sampled by bottom trawl surveys.

• Code by Zoë J. Kitchel

SESSION INFO TO DO

library(data.table)
library(vegan)
library(sf)
library(concaveman) #polygon around points
library(betapart) #allows us to partition beta diversity
library(geosphere)
library(ggpubr) #stat_regline_equation
library(nlme)
library(mgcv) #to make gam
library(cowplot)
library(lme4)

#Pull Dissimilarity Means
distances_dissimilarities_allyears.r <- readRDS(here::here("output","dissimilarities", "distances_dissimilarities_allyears.r.rds"))

#make survey and survey unit factors
distances_dissimilarities_allyears.r[,survey:=factor(survey)][,survey_unit:=factor(survey_unit)]

#adjust years
distances_dissimilarities_allyears.r[,year_adj := year-min(year)+1]

#add new variable for year in sequence per region
distances_dissimilarities_allyears.r[,first_year := min(year),.(survey_unit)]
distances_dissimilarities_allyears.r[,last_year := max(year),.(survey_unit)]

#distances_dissimilarities_allyears.r[,year_in_seq := year-first_year+1]

distances_dissimilarities_allyears.r[,years_sampled := last_year-first_year+1]

###Palette for Plotting Palette for plotting all 37 survey units

survey_unit.list <- levels(distances_dissimilarities_allyears.r[,survey_unit])

palette_42 <- c(
  "#5A5156", #AI
  "#DF00DB", #BITS-1
  "#DB8EDA", #BITS-4
  "#F6222E", #CHL
  "#F8A19F", #DFO-NF
  "#16FF32", #DFO-QCS
  "#325A9B", #EBS
  "#3283FE", #EVHOE
  "#FEAF16", #FR-CGFS
  "#fccb6d", #GMEX-Fall
  "#1C8356", #GMEX-Summer
  "#C4451C", #GOA
  "#85660D", #GRL-DE
  "#B0009F", #GSL-N
  "#BF79B8", #GSL-S
  "#1CBE4F", #ICE-GFS
  "#782AB6", #IE-IGFS
  "#90AD1C", #MEDITS
  "#6B003A", #NAM
  "#A75B00", #NEUS-Fall
  "#E3B072", #NEUS-Spring
  "#02E8B6", #NIGFS-1
  "#97E7D5", #NIGFS-4
  "#B00068", #Nor-BTS-3
  "#00B9E3", #NS-IBTS-1
  "#95E2F4", #NS-IBTS-3
  "#B3CE73", #NZ-CHAT
  "#689500", #NZ-ECSI
  "#364d02",#NZ-SUBA
  "#AAF400", #NZ-WCSI
  "#AA0DFE", #PT-IBTS
  "#7f9eb8", #ROCKALL
  "#FA0087", #S-GEORG
  "#DEA0FD", #SCS-Summer
  "#FCEF88", #SEUS-fall
  "#A59405", #SEUS-spring
  "#FCE100", #SEUS-summer
  "#544563", #SWC-IBTS-1
  "#a37fc7", #SWC-IBTS-4
  "#C075A6", #WCANN
  "#BDCDFF", #ZAF-ATL
  "#003EFF"  #ZAF-IND
)

color_link <- data.table(survey_unit = survey_unit.list,hex = palette_42)

Add names for plotting

name_helper <- data.table(Survey_Name_Season = c("Aleutian Islands",
                                    "Baltic Sea Q1",
                                    "Baltic Sea Q4",
                                    "Chile",
                                    "Newfoundland",
                                    "Queen Charlotte Sound",
                                    "Eastern Bering Sea",
                                    "Bay of Biscay",
                                    "English Channel",
                                    "Gulf of Mexico Summer",
                                    "Gulf of Alaska",
                                    "Greenland",
                                    "N Gulf of St. Lawrence",
                                    "S Gulf of St. Lawrence",
                                    "Iceland",
                                    "Irish Sea",
                                    "Mediterranean",
                                    "Namibia",
                                    "NE US Fall",
                                    "NE US Spring",
                                    "N Ireland Q1",
                                    "N Ireland Q4",
                                    "Barents Sea Norway Q3",
                                    "N Sea Q1",
                                    "N Sea Q3",
                                    "Chatham Rise NZ",
                                    "E Coast S Island NZ",
                                    "W Coast S Island NZ",
                                    "Portugal",
                                    "S Georgia",
                                  "Scotian Shelf Summer",
                                  "SE US Fall",
                                  "SE US Spring",
                                  "SE US Summer",
                                  "W Coast US",
                                  "Atlantic Ocean ZA",
                                  "Indian Ocean ZA",
                                   "Rockall Plateau",
                                  "Scotland Shelf Sea Q1",
                                  "Scotland Shelf Sea Q4",
                                  "Falkland Islands",
                                  "Gulf of Mexico Fall",
                                  "Barents Sea Norway Q1",
                                  "Sub-Arctic NZ",
                                  "Scotian Shelf Spring"),
                          survey_unit = c(
                                  "AI",        
                                  "BITS-1",    
                                  "BITS-4",    
                                  "CHL",       
                                  "DFO-NF",    
                                  "DFO-QCS",   
                                  "EBS",       
                                  "EVHOE",     
                                  "FR-CGFS",   
                                  "GMEX-Summer",
                                  "GOA",       
                                  "GRL-DE",    
                                  "GSL-N",     
                                  "GSL-S",     
                                  "ICE-GFS",   
                                  "IE-IGFS",   
                                  "MEDITS",    
                                  "NAM",       
                                  "NEUS-Fall", 
                                  "NEUS-Spring",
                                  "NIGFS-1",   
                                  "NIGFS-4",   
                                  "Nor-BTS-3", 
                                  "NS-IBTS-1", 
                                  "NS-IBTS-3", 
                                  "NZ-CHAT",   
                                  "NZ-ECSI",   
                                  "NZ-WCSI",   
                                  "PT-IBTS",   
                                  "S-GEORG",   
                                  "SCS-SUMMER",
                                  "SEUS-fall", 
                                  "SEUS-spring",
                                  "SEUS-summer",
                                  "WCANN",     
                                  "ZAF-ATL",   
                                  "ZAF-IND",
                                  "ROCKALL",
                                  "SWC-IBTS-1",
                                  "SWC-IBTS-4",
                                  "FALK",
                                  "GMEX-Fall",
                                  "Nor-BTS-1",
                                  "NZ-SUBA",
                                  "SCS-SPRING"
                          ))


color_link <- color_link[name_helper, on = "survey_unit"]

##Make GAMs

Jaccard

bray_curtis_total_gam <- gam(bray_curtis_dissimilarity_total_mean ~ year + s(survey_unit, year, bs = "fs", m = 1),#random smooth
                            data = distances_dissimilarities_allyears.r)

##Make LMERS

Bray These all converged

#running with lme instead of lmer gave same results, but allowed for calculation of p-value
bray_curtis_total_lme <- lme(bray_curtis_dissimilarity_total_mean ~ year_adj, random = (~1 + year_adj|survey_unit),data = distances_dissimilarities_allyears.r)

#but also run with lmer for confint
bray_curtis_total_lmer <- lmer(bray_curtis_dissimilarity_total_mean ~ year_adj + (1 + year_adj|survey_unit),data = distances_dissimilarities_allyears.r)

Warning: Model failed to converge with max|grad| = 0.137452 (tol = 0.002, component 1)

summary(bray_curtis_total_lme)

Linear mixed-effects model fit by REML
  Data: distances_dissimilarities_allyears.r 

Random effects:
 Formula: ~1 + year_adj | survey_unit
 Structure: General positive-definite, Log-Cholesky parametrization
            StdDev      Corr  
(Intercept) 0.108413092 (Intr)
year_adj    0.001972694 -0.763
Residual    0.023981944       

Fixed effects:  bray_curtis_dissimilarity_total_mean ~ year_adj 

 Correlation: 
         (Intr)
year_adj -0.791

Standardized Within-Group Residuals:
       Min         Q1        Med         Q3        Max 
-4.8791736 -0.4684941  0.0317567  0.5158154  4.3793155 

Number of Observations: 897
Number of Groups: 42 

anova(bray_curtis_total_lme)

bray_curtis_total_coefs <- data.table(coef(bray_curtis_total_lme))
bray_curtis_total_coefs[,survey_unit := rownames(coef(bray_curtis_total_lme))][,Year := round(year_adj,5)][,Intercept := round(`(Intercept)`,2)]
View(bray_curtis_total_coefs)

bray_curtis_total_coefs <- bray_curtis_total_coefs[color_link, on = "survey_unit"]

bray_curtis_total_coefs.exp <- bray_curtis_total_coefs[,.(Survey_Name_Season, Intercept, Year)]

#export this table
fwrite(bray_curtis_total_coefs.exp, file = here::here("output","bray_curtis_total_coefs.exp.csv"))

Get LMER model as predictions

# need to sort out year in seq versus overall year models
#new data for lmer
lmer_year <- seq(min(distances_dissimilarities_allyears.r[,year]), max(distances_dissimilarities_allyears.r[,year]), by = 0.1)

lmer_year_adj <- seq(min(distances_dissimilarities_allyears.r[,year_adj]), max(distances_dissimilarities_allyears.r[,year_adj]), by = 0.1)

#predict average lmer
lmer_bray_total_predictions <- data.table(year = lmer_year, year_adj = lmer_year_adj)

#confidence intervals
bray_curtis_total_lmer_confint <- confint(bray_curtis_total_lmer)

Computing profile confidence intervals ...

#populate data table of lmer predictions
lmer_bray_total_predictions[,bray_curtis_lmer_preds := fixef(bray_curtis_total_lmer)[[1]] + fixef(bray_curtis_total_lmer)[[2]] * year_adj][,bray_curtis_lmer_preds_lowerCI := bray_curtis_total_lmer_confint[5] + bray_curtis_total_lmer_confint[6] * year_adj][,bray_curtis_lmer_preds_upperCI := bray_curtis_total_lmer_confint[11] + bray_curtis_total_lmer_confint[12] * year_adj]

###Move forward with Jaccard Total (others to supplement)

Coefficients for LMER by survey_unit

#unique survey unit year combos
survey_unit_sampling_years <- unique(distances_dissimilarities_allyears.r[,.(survey_unit, year_adj, year, years_sampled)])

# see group coefficients
model_coefs_reduced <- data.table(transform(as.data.frame(ranef(bray_curtis_total_lmer)), lwr = condval - 1.96*condsd, upr = condval + 1.96*condsd))
#https://stackoverflow.com/questions/69805532/extract-the-confidence-intervals-of-lmer-random-effects-plotted-with-dotplotra


#ONLY SLOPES
model_coefs_reduced <- model_coefs_reduced[term == "year_adj",]

model_coefs_reduced[,survey_unit := grp][,year_adj := condval]

#merge with duration of survey
model_coefs_reduced_length <- model_coefs_reduced[survey_unit_sampling_years, on = "survey_unit"]


model_coefs_reduced_length[,years_sampled := as.numeric(years_sampled)][,Directional_Change := ifelse(year_adj > 0, "Differentiation","Homogenization")]

#does it cross zero?
model_coefs_reduced_length[,significant := ifelse(lwr >0 & upr>0,T,ifelse(lwr<0 & upr<0,T,F))]

#significant directional change
model_coefs_reduced_length[,Directional_Change_sig := ifelse(year_adj > 0 & significant == T, "Differentiation",ifelse(year_adj < 0 & significant == T, "Homogenization", "No trend in\ndissimilarity"))]


#min max distances_dissimilarities
min_bray_reduced <- min(distances_dissimilarities_allyears.r[,bray_curtis_dissimilarity_total_mean], na.rm = T)
max_bray_reduced <- max(distances_dissimilarities_allyears.r[,bray_curtis_dissimilarity_total_mean], na.rm = T)

model_coefs_reduced_length <- model_coefs_reduced_length[color_link, on = "survey_unit"]

#delete any NAs
model_coefs_reduced_length <- na.omit(model_coefs_reduced_length, cols = "significant")

#order table by coefficient
setorder(model_coefs_reduced_length, year_adj)

jaccard_total_model_coefs_reduced_length.unique <- unique(model_coefs_reduced_length[,.(condval,condsd, lwr, upr, survey_unit, year_adj, years_sampled, Directional_Change, hex, Survey_Name_Season, significant, Directional_Change_sig)]) 

#extract color hexes
#year adj coef order
color_year_adj_order <- jaccard_total_model_coefs_reduced_length.unique[,hex]

#alphabetical order
jaccard_total_model_coefs_reduced_length.unique.alpha <- setorder(jaccard_total_model_coefs_reduced_length.unique, Survey_Name_Season)

jaccard_total_model_coefs_reduced_length.unique.alpha[,trend_color := ifelse(Directional_Change_sig == "Homogenization", "#e7ac5b", ifelse(Directional_Change_sig == "Differentiation","#91c874","#cbbfde"))]

color_alpha_order <- jaccard_total_model_coefs_reduced_length.unique.alpha[,hex]
color_alpha_order_bytrend <- jaccard_total_model_coefs_reduced_length.unique.alpha[, trend_color]

saveRDS(jaccard_total_model_coefs_reduced_length.unique, here::here("output","region_stats","jaccard_total_model_coefs_reduced_length.unique.Rds"))

Bar Plot Coefficient LMER

jaccard_TOTAL_Dissimilarity_Coef_errorbar_reduced <- ggplot() +
    geom_errorbar(data = model_coefs_reduced_length, aes(x = reorder(Survey_Name_Season, year_adj) , y = year_adj, label = Survey_Name_Season, ymin = lwr, ymax = upr), fill = "grey", width = 0) + #add confidence intervals
  geom_point(data = model_coefs_reduced_length, aes(x = reorder(Survey_Name_Season, year_adj) , y = year_adj, label = Survey_Name_Season, size = years_sampled, fill = Directional_Change_sig, color = Directional_Change_sig), stat = 'identity', shape = 21) +
  scale_fill_manual(values = c("white","black","grey"), name = "Dissimilarity trend", guide="none") +
  scale_color_manual(values = c("black","black","grey"), name = "Dissimilarity trend", guide="none") +
  scale_size_binned(range = c(1,8), name = "Survey period length") +
  geom_hline(yintercept = 0) +
  scale_y_continuous(breaks = seq(-0.005, 0.0075, by = 0.0025), labels = c("-0.005","","0", "", "0.005",  "")) +
  xlab("Survey unit") +
  ylab("β-diversity trend") + #total jaccard dissimilarity trend
  coord_flip() +
  theme_classic() +
  theme(axis.text.y = element_text(colour = color_year_adj_order, face = "bold"), axis.title.y = element_blank(), axis.text.x = element_text(size = 15), axis.title.x = element_text(size = 15), legend.position = c(0.2,0.8), legend.direction = "vertical", legend.background = element_rect(fill = "transparent"))

Warning: Ignoring unknown parameters: `fill`Warning: Ignoring unknown aesthetics: labelWarning: Ignoring unknown aesthetics: labelWarning: Vectorized input to `element_text()` is not officially supported.
ℹ Results may be unexpected or may change in future versions of ggplot2.

#pull legend for homogenization
directional_change_legend_plot <- jaccard_TOTAL_Dissimilarity_Coef_errorbar_reduced + 
  scale_fill_manual(values = c("white","black","grey"), name = "Dissimilarity trend") +
  scale_color_manual(values = c("black","black","grey"), name = "Dissimilarity trend") +
  scale_size_binned(range = c(1,8), name = "Survey period length", guide = "none") +
  theme(legend.position = "right", legend.background = element_rect(fill= "transparent")) +
  guides(colour = guide_legend(override.aes = list(size=6)))

Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.Scale for size is already present.
Adding another scale for size, which will replace the existing scale.

jaccard_TOTAL_Dissimilarity_Coef_errorbar_reduced

#ALT grey scale
jaccard_TOTAL_Dissimilarity_Coef_errorbar_reduced_greyscale <- ggplot() +
    geom_errorbar(data = model_coefs_reduced_length, aes(x = reorder(Survey_Name_Season, year_adj) , y = year_adj, label = Survey_Name_Season, ymin = lwr, ymax = upr), fill = "grey", width = 0) + #add confidence intervals
  geom_point(data = model_coefs_reduced_length, aes(x = reorder(Survey_Name_Season, year_adj) , y = year_adj, label = Survey_Name_Season, size = years_sampled, fill = Directional_Change_sig, color = Directional_Change_sig), stat = 'identity', shape = 21) +
  scale_fill_manual(values = c("white","black","grey"), name = "Dissimilarity trend", guide="none") +
  scale_color_manual(values = c("black","black","grey"), name = "Dissimilarity trend", guide="none") +
  scale_size_binned(range = c(1,8), name = "Survey period length") +
  geom_hline(yintercept = 0) +
  scale_y_continuous(breaks = seq(-0.005, 0.0075, by = 0.0025), labels = c("-0.005","","0", "", "0.005",  "")) +
  xlab("Survey unit") +
  ylab("β-diversity trend") + #total jaccard dissimilarity trend
  coord_flip() +
  theme_classic() +
  theme(axis.text.y = element_text(face = "bold"), axis.title.y = element_blank(), axis.text.x = element_text(size = 15), axis.title.x = element_text(size = 15), legend.position = c(0.25,0.8), legend.direction = "vertical")

Warning: Ignoring unknown parameters: `fill`Warning: Ignoring unknown aesthetics: labelWarning: Ignoring unknown aesthetics: label

Alternatively, we color this plot by trend experienced

jaccard_total_Dissimilarity_Coef_errorbar_reduced_colorbytrend <- ggplot() +
    geom_errorbar(data = model_coefs_reduced_length, aes(x = reorder(Survey_Name_Season, year_adj) , y = year_adj, label = Survey_Name_Season, ymin = lwr, ymax = upr), fill = "grey", width = 0) + #add confidence intervals
  geom_point(data = model_coefs_reduced_length, aes(x = reorder(Survey_Name_Season, year_adj) , y = year_adj, label = Survey_Name_Season, size = years_sampled, color = Directional_Change_sig), stat = 'identity') +
  scale_color_manual(values = c("#73BA4D","#E0962C","#cbbfde"), name = "Dissimilarity trend", guide="none") +
  scale_size_binned(range = c(1,8), name = "Survey period length\n(years)") +
  geom_hline(yintercept = 0) +
  scale_y_continuous(breaks = seq(-0.005, 0.0075, by = 0.0025), labels = c("-0.005","","0", "", "0.005",  "")) +
  ylim(-0.015,0.006) +
  xlab("Survey unit") +
  ylab("β-diversity trend") + #total jaccard dissimilarity trend
  coord_flip() +
  theme_classic() +
  theme(axis.text.y = element_text(face = "bold"), axis.title.y = element_blank(), axis.text.x = element_text(size = 15), axis.title.x = element_text(size = 15), legend.position = c(0.25,0.8), legend.direction = "vertical", legend.text = element_text(size = 14), legend.title = element_text(size = 15), legend.background = element_rect(fill = "transparent"))

Warning: Ignoring unknown parameters: `fill`Warning: Ignoring unknown aesthetics: labelWarning: Ignoring unknown aesthetics: labelScale for y is already present.
Adding another scale for y, which will replace the existing scale.

Wavy Line Plot for GAMs

Generate predicted values

#add colors and names to full dissimilarity data table
distances_dissimilarities_allyears.r <- distances_dissimilarities_allyears.r[color_link, on = "survey_unit"]

#generate new data to smooth lines (need year and season survey combinations)
year_survey_unit_expand.dt <- data.table(survey_unit = as.character(NULL), year = as.numeric(NULL), year_adj = as.numeric(NULL ))

for (i in 1:length(survey_unit.list)) {
  #generate year vectors
  survey_unit_years <- unique(distances_dissimilarities_allyears.r[survey_unit == survey_unit.list[i],.(survey_unit, year, year_adj)])
  
  years <- seq(min(survey_unit_years[,year]), max(survey_unit_years[,year]), by = 0.1)
  
  year_adjust <- seq(min(survey_unit_years[,year_adj]), max(survey_unit_years[,year_adj]), by = 0.1)
  
  year_survey_unit_expand.dt_addition <- data.table(survey_unit = survey_unit.list[i], year = years, year_adj = year_adjust)
  
  year_survey_unit_expand.dt <- rbind(year_survey_unit_expand.dt, year_survey_unit_expand.dt_addition)
}

#add colors and names to full year and survey unit combination table
year_survey_unit_expand.dt <- year_survey_unit_expand.dt[color_link, on = "survey_unit"]

Get model as predictions

#for plotting, get model as predictions
bray_curtis_total_gam_predictions <- predict(bray_curtis_total_gam, se.fit = TRUE, newdata = year_survey_unit_expand.dt)

#merge into table
year_survey_unit_expand.dt[,bray_glm_mod_fit := bray_curtis_total_gam_predictions$fit][,bray_glm_mod_fit_SE := bray_curtis_total_gam_predictions$se.fit]

Produce Plot of GAM and mean LMER line

points_wavylines_bray_total_year_reduced_gam_nolmer <- ggplot() +
 # geom_ribbon(data = lmer_bray_total_predictions, aes(x = year, ymin = bray_curtis_lmer_preds_lowerCI, ymax = bray_curtis_lmer_preds_upperCI), fill = "grey", alpha = 0.2) +
  geom_point(data = na.omit(distances_dissimilarities_allyears.r,cols = "year_adj"),
             aes(x = year,
                 y = bray_curtis_dissimilarity_total_mean,
                 color = Survey_Name_Season), alpha = 0.5, size = 1) +
    geom_line(data = na.omit(year_survey_unit_expand.dt,cols = "year_adj"),
             aes(x = year,
                 y = bray_glm_mod_fit,
                 color = Survey_Name_Season)) +
  geom_ribbon(data = na.omit(year_survey_unit_expand.dt,cols = "year_adj"), aes(x = year, ymin=bray_glm_mod_fit-bray_glm_mod_fit_SE, ymax=bray_glm_mod_fit+bray_glm_mod_fit_SE, fill =  Survey_Name_Season), alpha=0.1) + #add standard error
 # geom_line(data = lmer_bray_total_predictions, aes(x = year, y = bray_curtis_lmer_preds), color = "black") +
    scale_color_manual(values =  color_alpha_order, name = "Survey Unit") +
  scale_fill_manual(values =  color_alpha_order, guide = "none") +
  theme_classic() +
  lims(x = c(min(distances_dissimilarities_allyears.r[,year]),max(distances_dissimilarities_allyears.r[,year])),
       y = c(0,0.5)) +
  xlab("Year") +
ylab("Total jaccard dissimilarity") +
  theme(legend.position = "null")

points_wavylines_bray_total_year_reduced_gam_nolmer

ggsave(points_wavylines_bray_total_year_reduced_gam_nolmer, path = here::here("figures"), filename ="points_wavylines_bray_total_year_reduced_gam_nolmer.jpg", height = 5, width = 5, unit = "in")

#with lmer

points_wavylines_bray_total_year_reduced_gam <- ggplot() +
  geom_ribbon(data = lmer_bray_total_predictions, aes(x = year, ymin = bray_curtis_lmer_preds_lowerCI, ymax = bray_curtis_lmer_preds_upperCI), fill = "grey", alpha = 0.3) +
  geom_point(data = na.omit(distances_dissimilarities_allyears.r, cols = "year_adj"),
             aes(x = year,
                 y = bray_curtis_dissimilarity_total_mean,
                 fill = Survey_Name_Season), alpha = 0.4, size = 1, shape = 21, color = "white") +
    geom_line(data = na.omit(year_survey_unit_expand.dt, cols = "year_adj"),
             aes(x = year,
                 y = bray_glm_mod_fit,
                 color = Survey_Name_Season), alpha = 0.6) +
  geom_ribbon(data = na.omit(year_survey_unit_expand.dt, cols = "year_adj"), aes(x = year, ymin=bray_glm_mod_fit-bray_glm_mod_fit_SE, ymax=bray_glm_mod_fit+bray_glm_mod_fit_SE, fill =  Survey_Name_Season), alpha=0.1) + #add standard error
  geom_line(data = lmer_bray_total_predictions, aes(x = year, y = bray_curtis_lmer_preds), color = "black") +
    scale_color_manual(values =  color_alpha_order, name = "Survey Unit") +
  scale_fill_manual(values =  color_alpha_order, guide = "none") +
  theme_classic() +
  lims(x = c(min(distances_dissimilarities_allyears.r[,year]),max(distances_dissimilarities_allyears.r[,year])),
       y = c(0,0.5)) +
  xlab("Year") +
ylab("β-diversity") +
  theme(legend.position = "null", axis.text = element_text(size = 15), axis.title = element_text(size = 15))

points_wavylines_bray_total_year_reduced_gam

ggsave(points_wavylines_bray_total_year_reduced_gam, path = here::here("figures"), filename ="points_wavylines_bray_total_year_reduced_gam.jpg", height = 6, width = 6, unit = "in")

#ALT
#plot all, but same color scheme (grey)
points_wavylines_bray_total_year_reduced_gam_greyscale <- ggplot() +
  geom_ribbon(data = lmer_bray_total_predictions, aes(x = year, ymin = bray_curtis_lmer_preds_lowerCI, ymax = bray_curtis_lmer_preds_upperCI), fill = "grey", alpha = 0.3) +
  geom_point(data = distances_dissimilarities_allyears.r,
             aes(x = year,
                 y = bray_curtis_dissimilarity_total_mean,
                 fill = Survey_Name_Season), alpha = 0.4, size = 1, shape = 21, color = "white") +
    geom_line(data = year_survey_unit_expand.dt,
             aes(x = year,
                 y = bray_glm_mod_fit,
                 color = Survey_Name_Season), alpha = 0.6) +
  geom_ribbon(data = year_survey_unit_expand.dt, aes(x = year, ymin=bray_glm_mod_fit-bray_glm_mod_fit_SE, ymax=bray_glm_mod_fit+bray_glm_mod_fit_SE, fill =  Survey_Name_Season), alpha=0.1) + #add standard error
  geom_line(data = lmer_bray_total_predictions, aes(x = year, y = bray_curtis_lmer_preds), color = "black") +
    scale_color_manual(values =  rep("black", times = length(unique(distances_dissimilarities_allyears.r$Survey_Name_Season))), name = "Survey Unit") +
  scale_fill_manual(values =  rep("black", times = length(unique(distances_dissimilarities_allyears.r$Survey_Name_Season))), guide = "none") +
  theme_classic() +
  lims(x = c(min(distances_dissimilarities_allyears.r[,year]),max(distances_dissimilarities_allyears.r[,year])),
       y = c(0,0.5)) +
  xlab("Year") +
ylab("β-diversity") +
  theme(legend.position = "null", axis.text = element_text(size = 15), axis.title = element_text(size = 15))

points_wavylines_bray_total_year_reduced_gam_greyscale

ggsave(points_wavylines_bray_total_year_reduced_gam_greyscale, path = here::here("figures"), filename ="points_wavylines_bray_total_year_reduced_gam_greyscale.jpg", height = 6, width = 6, unit = "in")

Alternative, color by trend

points_wavylines_bray_total_year_reduced_gam_colorbytrend <- ggplot() +
  geom_ribbon(data = lmer_bray_total_predictions, aes(x = year, ymin = bray_curtis_lmer_preds_lowerCI, ymax = bray_curtis_lmer_preds_upperCI), fill = "grey", alpha = 0.3) +
  geom_point(data = na.omit(distances_dissimilarities_allyears.r, cols = "year_adj"),
             aes(x = year,
                 y = bray_curtis_dissimilarity_total_mean,
                 fill = Survey_Name_Season), alpha = 0.4, size = 1, shape = 21, color = "white") +
    geom_line(data = na.omit(year_survey_unit_expand.dt, cols = "year_adj"),
             aes(x = year,
                 y = bray_glm_mod_fit,
                 color = Survey_Name_Season), alpha = 0.6) +
  geom_ribbon(data = na.omit(year_survey_unit_expand.dt, cols = "year_adj"), aes(x = year, ymin=bray_glm_mod_fit-bray_glm_mod_fit_SE, ymax=bray_glm_mod_fit+bray_glm_mod_fit_SE, fill =  Survey_Name_Season), alpha=0.1) + #add standard error
  geom_line(data = lmer_bray_total_predictions, aes(x = year, y = bray_curtis_lmer_preds), color = "black") +
    scale_color_manual(values =  color_alpha_order_bytrend, name = "Survey Unit") +
  scale_fill_manual(values =  color_alpha_order_bytrend, guide = "none") +
  theme_classic() +
  lims(x = c(min(distances_dissimilarities_allyears.r[,year]),max(distances_dissimilarities_allyears.r[,year]))) +
  xlab("Year") +
ylab("β-diversity") +
  theme(legend.position = "null", axis.text = element_text(size = 15), axis.title = element_text(size = 15))

points_wavylines_bray_total_year_reduced_gam_colorbytrend

ggsave(points_wavylines_bray_total_year_reduced_gam_colorbytrend, path = here::here("figures"), filename ="points_wavylines_bray_total_year_reduced_gam_colorbytrend.jpg", height = 6, width = 6, unit = "in")

#plot each independently for supplement
#all survey names = 
all_survey_names <- sort(unique(distances_dissimilarities_allyears.r$Survey_Name_Season))
#list of plots
points_wavylines_bray_total_year_reduced_gam_individual <- list()
for (i in 1:length(all_survey_names)) {
points_wavylines_bray_total_year_reduced_gam_individual[[i]] <- ggplot() +
  geom_point(data = distances_dissimilarities_allyears.r[Survey_Name_Season == all_survey_names[i]],
             aes(x = year,
                 y = bray_curtis_dissimilarity_total_mean), alpha = 0.4, color = "black") +
    geom_line(data = year_survey_unit_expand.dt[Survey_Name_Season == all_survey_names[i]],
             aes(x = year,
                 y = bray_glm_mod_fit), alpha = 0.6) +
  geom_ribbon(data = year_survey_unit_expand.dt[Survey_Name_Season == all_survey_names[i]], aes(x = year, ymin=bray_glm_mod_fit-bray_glm_mod_fit_SE, ymax=bray_glm_mod_fit+bray_glm_mod_fit_SE), alpha=0.1) + #add standard error
  theme_classic() +
#  lims(x = c(min(distances_dissimilarities_allyears.r[Survey_Name_Season == all_survey_names[i],year]),max(distances_dissimilarities_allyears.r[Survey_Name_Season == all_survey_names[i],year])),
#       y = c(0,0.5)) +
  xlab("Year") +
ylab("beta-diversity") +
  facet_wrap(~Survey_Name_Season, ncol = 5) +
  theme(legend.position = "null", axis.text = element_text(size = 15), axis.title = element_text(size = 15))

print(points_wavylines_bray_total_year_reduced_gam_individual[[i]])

}

saveRDS(points_wavylines_bray_total_year_reduced_gam_individual, here::here("figures","points_wavylines_bray_total_year_reduced_gam_individual.Rds"))

#print to pdf
library(gridExtra)

ggsave(
   filename = here::here("figures","points_wavylines_bray_total_year_reduced_gam_individual.pdf"), 
   plot = marrangeGrob(points_wavylines_bray_total_year_reduced_gam_individual, nrow=1, ncol=1), 
   width = 8.5, height = 11
)

Warning: Removed 1 rows containing missing values (`geom_point()`).Warning: Removed 1 row containing missing values (`geom_line()`).Warning: no non-missing arguments to max; returning -InfWarning: Removed 1 rows containing missing values (`geom_point()`).Warning: Removed 1 row containing missing values (`geom_line()`).Warning: no non-missing arguments to max; returning -InfWarning: Removed 1 rows containing missing values (`geom_point()`).Warning: Removed 1 row containing missing values (`geom_line()`).Warning: no non-missing arguments to max; returning -Inf

Merge jaccard versus Year plot with GAMS and Region vs. coefficient plot for LMERs